plotRegions: Plot user-provided regions.
In charm: Analysis of DNA methylation data from CHARM microarrays

Description Usage Arguments Details Author(s) See Also Examples

Plot user-provided regions.

plotRegions(thetable, cleanp, chr, pos, seq=NULL, Genome, cpg.islands, exposure, exposure.continuous=FALSE, outfile="./myregions.pdf", which_lines=NULL, which_points=which_lines, ADD=3000, cols=c("black","red","blue","gray","green","orange","brown"), legend.size=1, smoo="loess", SPAN=300, DELTA=36, panel3="none", G=NULL, grs=NULL)

`thetable`	a table with columns for "chr","start", and "end", identifying the genomic regions to plot (if they are covered on the array).
`cleanp`	the matrix of percent methylation estimates to be used for plotting
`chr`	vector of chromosome labels for the probes in cleanp
`pos`	vector of chromosomal coordinates for the probes in cleanp
`seq`	vector of probe sequences corresponding to the rows of G (and cleanp). Needed only if panel3="G".
`Genome`	the BSgenome object for the organism based upon which your array was designed.
`cpg.islands`	a table with columns "chr","start", and "end" for CpG islands to plot in the second panel.
`outfile`	the name of the file to save (including the full path)
`exposure`	The covariate of interest.
`exposure.continuous`	set to TRUE if exposure is a continuous variable.
`which_lines`	vector specifying which groups (unique elements of exposure) to plot the lines for. If NULL (the default), plots lines for all groups. Only applies if exposure is categorical.
`which_points`	vector specifying which groups (unique elements of exposure) to plot the points for. If NULL (the default), plots points for all groups. Only applies if exposure is categorical.
`ADD`	Number of base pairs to plot on either side of each DMR candidate (if it is covered on the array).
`cols`	vector of colors to use, one for each group (if covariate is categorical)
`legend.size`	magnification factor for the legend
`smoo`	"loess" for loess smoother or "runmed" for running median smoother (runmed with k=3).
`SPAN`	see DELTA. Only used if smoo="loess"
`DELTA`	span parameter in loess smoothing will = SPAN/(DELTA * number of probes in the plotted region). Only used if smoo="loess".
`panel3`	if panel3="G", the third panel of each DMR plot will show the difference between the median green channel value (after subtracting probe medians and correcting for gc content) between the 2 groups (i.e., the group defined by mod[,coef] in dmrFind minus the reference group). If panel="G", seq argument must be provided. If panel!="G", the 3rd panel will show -log10(dmrs$pval).
`G`	matrix of green channel intensities to use for plotting in the 3rd panel if panel3="G".
`grs`	if panel3="G", plot difference between the median green channel value (after subtracting probe medians and correcting for gc content) between these 2 groups.